Starting phenix.real_space_refine on Wed Feb 12 08:44:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xow_22282/02_2025/6xow_22282.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xow_22282/02_2025/6xow_22282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xow_22282/02_2025/6xow_22282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xow_22282/02_2025/6xow_22282.map" model { file = "/net/cci-nas-00/data/ceres_data/6xow_22282/02_2025/6xow_22282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xow_22282/02_2025/6xow_22282.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4904 2.51 5 N 1307 2.21 5 O 1461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7711 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7711 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 966, 7697 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 966, 7697 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901} Chain breaks: 1 bond proxies already assigned to first conformer: 7872 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 residue: pdb=" N AASN A 915 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN A 915 " occ=0.41 Time building chain proxies: 7.53, per 1000 atoms: 0.98 Number of scatterers: 7711 At special positions: 0 Unit cell: (87.21, 87.21, 97.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1461 8.00 N 1307 7.00 C 4904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 54.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 101 through 111 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.775A pdb=" N LYS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.909A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.573A pdb=" N ILE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 4.852A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 466 through 481 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 528 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 608 through 613 Proline residue: A 613 - end of helix Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 631 through 643 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 695 through 713 Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.865A pdb=" N HIS A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.200A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 902 Processing helix chain 'A' and resid 928 through 945 removed outlier: 3.512A pdb=" N LEU A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 964 Processing helix chain 'A' and resid 973 through 980 removed outlier: 3.808A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.693A pdb=" N LYS A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1009 Processing helix chain 'A' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.227A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 63 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 75 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N MET A 135 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 149 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.227A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 63 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 75 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313 removed outlier: 6.298A pdb=" N ARG A 307 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER A 503 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE A 309 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ARG A 505 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 311 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 328 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN A 394 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL A 330 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLY A 392 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE A 332 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N SER A 390 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 334 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR A 388 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP A 336 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLU A 386 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 381 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 390 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 579 removed outlier: 7.402A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 667 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 576 through 579 removed outlier: 7.402A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912 removed outlier: 3.889A pdb=" N VAL A 866 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS A 854 " --> pdb=" O ILE A1035 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG A1037 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N HIS A 856 " --> pdb=" O ARG A1037 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2455 1.33 - 1.45: 1286 1.45 - 1.57: 4101 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7904 Sorted by residual: bond pdb=" CG ARG A 545 " pdb=" CD ARG A 545 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.86e+00 bond pdb=" CB GLN A 91 " pdb=" CG GLN A 91 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" N ILE A 724 " pdb=" CA ILE A 724 " ideal model delta sigma weight residual 1.460 1.443 0.017 1.21e-02 6.83e+03 1.87e+00 bond pdb=" CA GLY A 644 " pdb=" C GLY A 644 " ideal model delta sigma weight residual 1.514 1.496 0.019 1.41e-02 5.03e+03 1.74e+00 bond pdb=" CA THR A 144 " pdb=" CB THR A 144 " ideal model delta sigma weight residual 1.532 1.508 0.024 1.82e-02 3.02e+03 1.69e+00 ... (remaining 7899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 10344 2.31 - 4.61: 306 4.61 - 6.92: 57 6.92 - 9.23: 10 9.23 - 11.53: 3 Bond angle restraints: 10720 Sorted by residual: angle pdb=" C TYR A 614 " pdb=" N VAL A 615 " pdb=" CA VAL A 615 " ideal model delta sigma weight residual 120.24 123.48 -3.24 6.30e-01 2.52e+00 2.64e+01 angle pdb=" C ILE A 899 " pdb=" N ARG A 900 " pdb=" CA ARG A 900 " ideal model delta sigma weight residual 120.88 114.63 6.25 1.62e+00 3.81e-01 1.49e+01 angle pdb=" CB MET A 749 " pdb=" CG MET A 749 " pdb=" SD MET A 749 " ideal model delta sigma weight residual 112.70 101.17 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CA TYR A 492 " pdb=" CB TYR A 492 " pdb=" CG TYR A 492 " ideal model delta sigma weight residual 113.90 107.22 6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" N GLU A 709 " pdb=" CA GLU A 709 " pdb=" CB GLU A 709 " ideal model delta sigma weight residual 110.16 115.32 -5.16 1.48e+00 4.57e-01 1.21e+01 ... (remaining 10715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4413 17.91 - 35.83: 294 35.83 - 53.74: 46 53.74 - 71.65: 18 71.65 - 89.56: 10 Dihedral angle restraints: 4781 sinusoidal: 1955 harmonic: 2826 Sorted by residual: dihedral pdb=" CA ALA A 319 " pdb=" C ALA A 319 " pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLN A 394 " pdb=" C GLN A 394 " pdb=" N GLY A 395 " pdb=" CA GLY A 395 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ARG A 129 " pdb=" C ARG A 129 " pdb=" N SER A 130 " pdb=" CA SER A 130 " ideal model delta harmonic sigma weight residual 180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 4778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 733 0.044 - 0.089: 324 0.089 - 0.133: 100 0.133 - 0.177: 15 0.177 - 0.222: 2 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CA TYR A 163 " pdb=" N TYR A 163 " pdb=" C TYR A 163 " pdb=" CB TYR A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE A1020 " pdb=" CA ILE A1020 " pdb=" CG1 ILE A1020 " pdb=" CG2 ILE A1020 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA LYS A 437 " pdb=" N LYS A 437 " pdb=" C LYS A 437 " pdb=" CB LYS A 437 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 1171 not shown) Planarity restraints: 1401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 303 " -0.033 2.00e-02 2.50e+03 2.63e-02 1.73e+01 pdb=" CG TRP A 303 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 303 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 303 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 303 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 303 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 303 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 303 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 303 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 314 " -0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 315 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 242 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO A 243 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.042 5.00e-02 4.00e+02 ... (remaining 1398 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 117 2.57 - 3.15: 7115 3.15 - 3.74: 12800 3.74 - 4.32: 17159 4.32 - 4.90: 26933 Nonbonded interactions: 64124 Sorted by model distance: nonbonded pdb=" OG1 THR A 872 " pdb=" O GLY A 916 " model vdw 1.991 3.040 nonbonded pdb=" O ASP A 377 " pdb=" OG SER A 390 " model vdw 2.033 3.040 nonbonded pdb=" OD2 ASP A 336 " pdb=" OG1 THR A 338 " model vdw 2.060 3.040 nonbonded pdb=" ND1 HIS A 186 " pdb=" O THR A 194 " model vdw 2.070 3.120 nonbonded pdb=" O ILE A 803 " pdb=" NH1 ARG A 805 " model vdw 2.089 3.120 ... (remaining 64119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.260 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7904 Z= 0.409 Angle : 0.998 11.533 10720 Z= 0.543 Chirality : 0.053 0.222 1174 Planarity : 0.007 0.098 1401 Dihedral : 13.389 89.563 2953 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.26), residues: 968 helix: -0.40 (0.22), residues: 458 sheet: 0.30 (0.38), residues: 176 loop : -1.35 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.006 TRP A 303 HIS 0.012 0.002 HIS A 498 PHE 0.024 0.003 PHE A 138 TYR 0.032 0.003 TYR A 597 ARG 0.016 0.002 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7623 (t80) cc_final: 0.7296 (t80) REVERT: A 266 PHE cc_start: 0.7046 (t80) cc_final: 0.6057 (t80) REVERT: A 436 MET cc_start: 0.9288 (mtp) cc_final: 0.8949 (mtt) REVERT: A 454 CYS cc_start: 0.8124 (t) cc_final: 0.7782 (p) REVERT: A 667 LEU cc_start: 0.9016 (tp) cc_final: 0.8585 (tp) REVERT: A 702 LEU cc_start: 0.9307 (mt) cc_final: 0.9061 (pp) REVERT: A 917 ILE cc_start: 0.7541 (mm) cc_final: 0.7304 (mm) REVERT: A 985 MET cc_start: 0.7967 (mpp) cc_final: 0.6747 (mpp) REVERT: A 1037 ARG cc_start: 0.7777 (mmt90) cc_final: 0.7224 (mmm160) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2059 time to fit residues: 36.8089 Evaluate side-chains 77 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 45 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN A 495 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 976 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.034354 restraints weight = 231926.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.036167 restraints weight = 119644.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037458 restraints weight = 79131.526| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7904 Z= 0.253 Angle : 0.791 9.728 10720 Z= 0.414 Chirality : 0.048 0.236 1174 Planarity : 0.007 0.083 1401 Dihedral : 5.558 19.436 1039 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.23 % Allowed : 3.14 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.27), residues: 968 helix: 0.43 (0.23), residues: 464 sheet: 0.32 (0.38), residues: 176 loop : -1.15 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 303 HIS 0.009 0.001 HIS A 276 PHE 0.020 0.002 PHE A 935 TYR 0.030 0.002 TYR A 597 ARG 0.007 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9472 (t80) cc_final: 0.8964 (t80) REVERT: A 212 ASP cc_start: 0.9412 (t0) cc_final: 0.9212 (t0) REVERT: A 265 PHE cc_start: 0.9701 (m-80) cc_final: 0.9345 (m-80) REVERT: A 450 TYR cc_start: 0.9021 (t80) cc_final: 0.8722 (t80) REVERT: A 454 CYS cc_start: 0.9767 (t) cc_final: 0.9436 (p) REVERT: A 598 PHE cc_start: 0.8813 (t80) cc_final: 0.8604 (t80) REVERT: A 702 LEU cc_start: 0.9831 (mt) cc_final: 0.9569 (pp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1755 time to fit residues: 27.4031 Evaluate side-chains 80 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032697 restraints weight = 218392.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.034324 restraints weight = 119102.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.035548 restraints weight = 80747.563| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7904 Z= 0.248 Angle : 0.726 8.483 10720 Z= 0.375 Chirality : 0.046 0.217 1174 Planarity : 0.006 0.073 1401 Dihedral : 5.263 17.728 1039 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.35 % Allowed : 2.21 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 968 helix: 0.47 (0.23), residues: 474 sheet: 0.24 (0.39), residues: 173 loop : -1.00 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 303 HIS 0.009 0.001 HIS A 69 PHE 0.024 0.002 PHE A 217 TYR 0.027 0.002 TYR A 597 ARG 0.006 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9306 (t80) cc_final: 0.8712 (t80) REVERT: A 206 MET cc_start: 0.9297 (mmp) cc_final: 0.8865 (ptp) REVERT: A 265 PHE cc_start: 0.9622 (m-80) cc_final: 0.9324 (m-80) REVERT: A 361 PHE cc_start: 0.9572 (m-80) cc_final: 0.8891 (m-80) REVERT: A 450 TYR cc_start: 0.9067 (t80) cc_final: 0.8791 (t80) REVERT: A 702 LEU cc_start: 0.9819 (mt) cc_final: 0.9572 (pp) REVERT: A 710 LEU cc_start: 0.9456 (mt) cc_final: 0.9058 (tp) REVERT: A 918 PHE cc_start: 0.9607 (t80) cc_final: 0.9359 (t80) REVERT: A 1037 ARG cc_start: 0.8866 (mmt90) cc_final: 0.8253 (mmm160) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1702 time to fit residues: 23.8097 Evaluate side-chains 67 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032187 restraints weight = 211662.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.033824 restraints weight = 115156.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035101 restraints weight = 77854.911| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7904 Z= 0.238 Angle : 0.703 8.732 10720 Z= 0.364 Chirality : 0.045 0.174 1174 Planarity : 0.006 0.067 1401 Dihedral : 5.094 16.127 1039 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.23 % Allowed : 1.75 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 968 helix: 0.54 (0.23), residues: 473 sheet: 0.11 (0.38), residues: 174 loop : -0.83 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 303 HIS 0.010 0.001 HIS A 498 PHE 0.016 0.002 PHE A 935 TYR 0.022 0.002 TYR A 492 ARG 0.005 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9243 (mmp) cc_final: 0.8759 (ptp) REVERT: A 265 PHE cc_start: 0.9592 (m-80) cc_final: 0.9377 (m-80) REVERT: A 353 LEU cc_start: 0.9760 (mt) cc_final: 0.9557 (mt) REVERT: A 361 PHE cc_start: 0.9596 (m-80) cc_final: 0.8776 (m-80) REVERT: A 450 TYR cc_start: 0.9117 (t80) cc_final: 0.8791 (t80) REVERT: A 553 ASP cc_start: 0.9089 (t0) cc_final: 0.8824 (t70) REVERT: A 702 LEU cc_start: 0.9849 (mt) cc_final: 0.9598 (pp) REVERT: A 1037 ARG cc_start: 0.8947 (mmt90) cc_final: 0.8482 (mmt90) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1700 time to fit residues: 22.9895 Evaluate side-chains 68 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 0.0870 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.031739 restraints weight = 254991.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033419 restraints weight = 127175.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.034797 restraints weight = 83948.005| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7904 Z= 0.205 Angle : 0.680 8.480 10720 Z= 0.348 Chirality : 0.044 0.160 1174 Planarity : 0.006 0.067 1401 Dihedral : 4.974 17.300 1039 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.23 % Allowed : 1.86 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 968 helix: 0.73 (0.23), residues: 471 sheet: 0.18 (0.39), residues: 167 loop : -0.76 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 303 HIS 0.008 0.001 HIS A 498 PHE 0.020 0.002 PHE A 124 TYR 0.019 0.001 TYR A 492 ARG 0.007 0.001 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9184 (mmp) cc_final: 0.8705 (ptm) REVERT: A 353 LEU cc_start: 0.9768 (mt) cc_final: 0.9542 (mt) REVERT: A 361 PHE cc_start: 0.9574 (m-80) cc_final: 0.8726 (m-80) REVERT: A 450 TYR cc_start: 0.9118 (t80) cc_final: 0.8778 (t80) REVERT: A 702 LEU cc_start: 0.9821 (mt) cc_final: 0.9566 (pp) REVERT: A 708 GLN cc_start: 0.9356 (mp10) cc_final: 0.9124 (pt0) REVERT: A 749 MET cc_start: 0.9114 (ppp) cc_final: 0.8910 (ppp) REVERT: A 1037 ARG cc_start: 0.9027 (mmt90) cc_final: 0.8493 (mmt90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1747 time to fit residues: 22.8686 Evaluate side-chains 68 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.032698 restraints weight = 146601.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.034088 restraints weight = 92311.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.035185 restraints weight = 67060.879| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7904 Z= 0.204 Angle : 0.671 8.020 10720 Z= 0.345 Chirality : 0.044 0.157 1174 Planarity : 0.005 0.066 1401 Dihedral : 4.849 18.680 1039 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.23 % Allowed : 1.63 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 968 helix: 0.92 (0.24), residues: 459 sheet: 0.03 (0.39), residues: 170 loop : -0.62 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 303 HIS 0.006 0.001 HIS A 498 PHE 0.025 0.002 PHE A 688 TYR 0.019 0.001 TYR A 492 ARG 0.005 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9118 (t80) cc_final: 0.8892 (t80) REVERT: A 206 MET cc_start: 0.9187 (mmp) cc_final: 0.8785 (ptp) REVERT: A 265 PHE cc_start: 0.9592 (m-80) cc_final: 0.9320 (m-80) REVERT: A 353 LEU cc_start: 0.9765 (mt) cc_final: 0.9528 (mt) REVERT: A 361 PHE cc_start: 0.9584 (m-80) cc_final: 0.8733 (m-80) REVERT: A 450 TYR cc_start: 0.9124 (t80) cc_final: 0.8764 (t80) REVERT: A 598 PHE cc_start: 0.8812 (t80) cc_final: 0.8605 (t80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1699 time to fit residues: 21.6365 Evaluate side-chains 64 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.030797 restraints weight = 207250.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032346 restraints weight = 115104.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.033556 restraints weight = 78901.590| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7904 Z= 0.247 Angle : 0.702 8.527 10720 Z= 0.366 Chirality : 0.044 0.163 1174 Planarity : 0.005 0.068 1401 Dihedral : 4.982 21.603 1039 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.23 % Allowed : 0.81 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 968 helix: 0.74 (0.24), residues: 465 sheet: 0.01 (0.38), residues: 171 loop : -0.69 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 303 HIS 0.007 0.001 HIS A 78 PHE 0.018 0.002 PHE A 124 TYR 0.024 0.002 TYR A 492 ARG 0.010 0.001 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.9235 (t80) cc_final: 0.8983 (t80) REVERT: A 206 MET cc_start: 0.9124 (mmp) cc_final: 0.8697 (ptp) REVERT: A 265 PHE cc_start: 0.9564 (m-80) cc_final: 0.9235 (m-80) REVERT: A 353 LEU cc_start: 0.9777 (mt) cc_final: 0.9540 (mt) REVERT: A 361 PHE cc_start: 0.9577 (m-80) cc_final: 0.8817 (m-80) REVERT: A 450 TYR cc_start: 0.9189 (t80) cc_final: 0.8955 (t80) REVERT: A 778 MET cc_start: 0.8662 (tpt) cc_final: 0.8416 (mmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1627 time to fit residues: 19.5162 Evaluate side-chains 60 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 95 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 10 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.041522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.029829 restraints weight = 198452.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.031287 restraints weight = 114184.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032416 restraints weight = 79176.546| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7904 Z= 0.270 Angle : 0.722 8.692 10720 Z= 0.376 Chirality : 0.045 0.157 1174 Planarity : 0.006 0.067 1401 Dihedral : 5.172 29.370 1039 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.23 % Allowed : 0.70 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 968 helix: 0.48 (0.23), residues: 463 sheet: -0.28 (0.39), residues: 174 loop : -0.58 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 303 HIS 0.007 0.002 HIS A 259 PHE 0.018 0.002 PHE A 169 TYR 0.023 0.002 TYR A 492 ARG 0.007 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 PHE cc_start: 0.9594 (m-80) cc_final: 0.9262 (m-80) REVERT: A 344 PHE cc_start: 0.9531 (t80) cc_final: 0.9207 (t80) REVERT: A 361 PHE cc_start: 0.9612 (m-80) cc_final: 0.9090 (m-80) REVERT: A 450 TYR cc_start: 0.9078 (t80) cc_final: 0.8833 (t80) REVERT: A 598 PHE cc_start: 0.8824 (t80) cc_final: 0.8620 (t80) REVERT: A 680 MET cc_start: 0.9620 (ppp) cc_final: 0.9407 (ppp) REVERT: A 681 MET cc_start: 0.9653 (ppp) cc_final: 0.9441 (ppp) REVERT: A 778 MET cc_start: 0.8760 (tpt) cc_final: 0.8428 (mmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1695 time to fit residues: 20.3299 Evaluate side-chains 58 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.030338 restraints weight = 172808.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.031730 restraints weight = 103955.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.032812 restraints weight = 73923.067| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7904 Z= 0.239 Angle : 0.701 8.559 10720 Z= 0.363 Chirality : 0.045 0.176 1174 Planarity : 0.006 0.079 1401 Dihedral : 5.184 31.930 1039 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.23 % Allowed : 0.00 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 968 helix: 0.49 (0.24), residues: 464 sheet: -0.32 (0.39), residues: 174 loop : -0.50 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 303 HIS 0.008 0.002 HIS A 78 PHE 0.016 0.002 PHE A 688 TYR 0.021 0.002 TYR A 492 ARG 0.006 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9189 (mmp) cc_final: 0.8807 (ptp) REVERT: A 265 PHE cc_start: 0.9558 (m-80) cc_final: 0.9232 (m-80) REVERT: A 361 PHE cc_start: 0.9596 (m-80) cc_final: 0.9121 (m-80) REVERT: A 450 TYR cc_start: 0.9081 (t80) cc_final: 0.8828 (t80) REVERT: A 680 MET cc_start: 0.9590 (ppp) cc_final: 0.9362 (ppp) REVERT: A 743 MET cc_start: 0.9616 (tpt) cc_final: 0.9408 (mmm) REVERT: A 778 MET cc_start: 0.8858 (tpt) cc_final: 0.8562 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1796 time to fit residues: 21.2497 Evaluate side-chains 58 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 61 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.029788 restraints weight = 266176.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.031474 restraints weight = 132647.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.032817 restraints weight = 86517.310| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7904 Z= 0.193 Angle : 0.674 7.983 10720 Z= 0.344 Chirality : 0.044 0.155 1174 Planarity : 0.005 0.074 1401 Dihedral : 4.964 30.381 1039 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.23 % Allowed : 0.12 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 968 helix: 0.70 (0.24), residues: 466 sheet: -0.33 (0.39), residues: 172 loop : -0.46 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 303 HIS 0.007 0.001 HIS A 78 PHE 0.016 0.002 PHE A 935 TYR 0.021 0.002 TYR A 597 ARG 0.005 0.001 ARG A 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9164 (mmp) cc_final: 0.8818 (ptp) REVERT: A 265 PHE cc_start: 0.9618 (m-80) cc_final: 0.9237 (m-80) REVERT: A 344 PHE cc_start: 0.9573 (t80) cc_final: 0.9328 (t80) REVERT: A 361 PHE cc_start: 0.9600 (m-80) cc_final: 0.9149 (m-80) REVERT: A 450 TYR cc_start: 0.8941 (t80) cc_final: 0.8686 (t80) REVERT: A 680 MET cc_start: 0.9536 (ppp) cc_final: 0.9332 (ppp) REVERT: A 743 MET cc_start: 0.9599 (tpt) cc_final: 0.9388 (mmm) REVERT: A 778 MET cc_start: 0.8913 (tpt) cc_final: 0.8572 (mmm) REVERT: A 853 MET cc_start: 0.9140 (mmp) cc_final: 0.8932 (mpp) REVERT: A 985 MET cc_start: 0.8948 (mpp) cc_final: 0.8742 (mpp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1710 time to fit residues: 20.8390 Evaluate side-chains 63 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.030406 restraints weight = 227481.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.031997 restraints weight = 121164.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033286 restraints weight = 81374.972| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7904 Z= 0.181 Angle : 0.658 7.784 10720 Z= 0.334 Chirality : 0.044 0.155 1174 Planarity : 0.005 0.074 1401 Dihedral : 4.812 29.581 1039 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.23 % Allowed : 0.12 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.28), residues: 968 helix: 0.85 (0.24), residues: 467 sheet: -0.30 (0.39), residues: 172 loop : -0.37 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 303 HIS 0.007 0.001 HIS A 78 PHE 0.016 0.002 PHE A 688 TYR 0.021 0.001 TYR A 597 ARG 0.005 0.001 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.98 seconds wall clock time: 44 minutes 12.97 seconds (2652.97 seconds total)